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New data collected from twenty-six sites during 2008 inthe contaminated Site of National Interest (SIN) of Porto Marghera within the Lagoon of Venice (Italy), which has been affected by the presence of an industrial zone for the last 80 years, were compared with data from a campaign performed in the same site 30 years before (1976-1978). The SIN was found to be heavily polluted in the earlier study, and several tons of Hg and Zn are still stored in soils and industrial channel sediments, potentially affecting the lagoon part of the SIN. Bathymetric variations, grain-size, Hg and Zn content in sediments were analysed. The severe contamination of the late 1970s (Hg 1.7 μg/g; Zn 754 μg/g) had fallen by the late 2000s (Hg 0.9 μg/g; Zn 225 μg/g). The fall in Hg and Zn contamination over the 30-year period was mainly linked to the patterns of geomorphological change inside the SIN that affected two distinct sub-areas: 1) a stable-depositional (SD) area in the Northern part, which exerted a “dilution” effect on contaminants, with significant deposition (~11%) of coarse-grained sediments (63 - 8 μm), and 2) an area characterised by moderate-to-severe-erosion (MSE) to the South, which saw the loss (~13%) of pollutant-bearing fine-grained sediments (<8 μm). A budget calculation in the MSE sub-area showed a loss of ~2.5 tons for Hg and ~700 tons for Zn over three decades, most of which was exported to other parts of the LV or at the open sea. A similar amount is still stored in the SD area, which will be subject to erosion if hydrodynamic conditions change in the future. This study provides useful support to decision-making systems by helping to select hot-spots for remediation measures.